hello SierraNevadaStar! I can't answer your questions but can only offer my own contemplation in addition to yours lol so hope you don't mind..
I don't know about crystals causing bad or negative experiences, some say they do but I personally don't know and think if they do it is for our own good I guess.. just like we cannot get out of the dark without piercing through it with light, and most of our paths would not be paved if it weren't for seemingly negative experiences.. so I could see how it'd make sense fro smoky quartz to work like that, especially if you are purposely using it for shadow work.
Shadow work has to do with facing and seeing our shadows or darkness that unnecessarily encompasses us, and your ultimate distaste of this smoky experience is your increased overthinking patterns, which shows an increase of consciousness, which obviously can be faced with more consciousness to dissolve it and thus you end up elevating yourself past that level or tendency to overthink or be bothered by the mind. I mean I'm sure all the monks and meditating gurus and stuff had quite a few thoughts and ingrained habits to squash and overcome before they were able to achieve prolonged mind clarity and inner peace, right? So as long as you are aware of something, it is not really a threat.. and you can deal with this and bring yourself out on a higher plane of existence afterwards.
The thing about your worst fears being realized in your dreams also seems to indicate that your desire for deep shadow working has been actualized and these are basically gifts for you to open and do whatever you want with the contents.. perhaps regift them to the higher good or that special place in the center of the Earth where unwanted things are transmuted into positive energy the Earth or Universe can use for something better.. or just face them and let them dissolve, I don't know, what do you think? and if you feel like sharing here what those worst fears are go right ahead. I wrote a poem about people giving me their fears before so I could do something cool with them but I'm sorry I forgot what it went like.. here is another one I made up lol forgive the cheesiness hope it dispels your uneasiness
give me all your fear my dear
I'll help you make it crystal clear
those murky waters needn't drown you
I'll put you back just how I found you
Another suggestion I have for you is to try using something like EFT in conjunction with or as a clean-up crew for your smoky quartz experience. EFT is a simple yet profound technique that apparently works on some deep levels and layers, and is even scientifically researched, validated for a variety of issues ranging from everyday to serious such as ptsd.. and it also has been shown to alter brain activity beneficially, according to those squiggly line machinery tests or whatever those are called..
If I were you I would keep working with smoky quartz, but I don't know maybe that was all it's meant to teach and open you to at this time, however I would stick with it at least a little longer as to not make it another unnecessary fear you know? that's good you're leaning toward staying with it. What about other crystals? have you been using any others prominently throughout this? How about pairing another crystal with it and see what kinds of results and dreams you get then? I mean the EFT or other energy work and various types of healing could be adequate or perfect, but another extra crystal or two might be just what the doctor ordered too. that'd be up to you but just for fun I'm gonna suggest a few.. well I was thinking a lot about selenite recently and it wants me to tell you so maybe that would be a cool one to pair with smoky quartz, cuz they are practically opposites, you know? what about rose quartz or turquoise if you have that.. I'm not sure what crystals you have, there could be so many options. maybe do chakra work along with the smoky.. but something aqua, blue or green might be a good choice to help calm the mental activity and help you open the heart more to receive the messages and accept them with love more easily. what do you think?